[English] 日本語
Yorodumi- PDB-1c6y: ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c6y | ||||||
---|---|---|---|---|---|---|---|
Title | ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP. | ||||||
Components | PROTEIN (PROTEASE) | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Munshi, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: An alternate binding site for the P1-P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease. Authors: Munshi, S. / Chen, Z. / Yan, Y. / Li, Y. / Olsen, D.B. / Schock, H.B. / Galvin, B.B. / Dorsey, B. / Kuo, L.C. #1: Journal: J.Biol.Chem. / Year: 1994 Title: Crystal Structure at 1.9-A Resolution of Human Immunodeficiency Virus (HIV) II Protease Complexed with L-735,524, an Orally Bioavailable Inhibitor of the HIV Proteases Authors: Chen, Z. / Li, Y. / Chen, E. / Hall, D.L. / Darke, P.L. / Culberson, C. / Shafer, J.A. / Kuo, L.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1c6y.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1c6y.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 1c6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c6y_validation.pdf.gz | 483.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1c6y_full_validation.pdf.gz | 486.5 KB | Display | |
Data in XML | 1c6y_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1c6y_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/1c6y ftp://data.pdbj.org/pub/pdb/validation_reports/c6/1c6y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10801.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NY5 ISOLATE / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: NY5 ISOLATE / Production host: Escherichia coli (E. coli) References: UniProt: O09893, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | ChemComp-MK1 / | #3: Water | ChemComp-HOH / | Nonpolymer details | L-735,524 IS N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)- TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL) ...L-735,524 IS N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)- TERTIARY BUTYLAMINO | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.98 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Details: THE CRYSTAL WAS PREPARED WITH CO CRYSTALLIZATION METHOD. 9X MUTANT PROTEASE HAS NINE POINT MUTATIONS COMPARED TO WILD TYPE: L10V,K20M,L24I,S37D,M46I,I54V,L63P,A71V,V82T THERE IS ONE PROTEASE ...Details: THE CRYSTAL WAS PREPARED WITH CO CRYSTALLIZATION METHOD. 9X MUTANT PROTEASE HAS NINE POINT MUTATIONS COMPARED TO WILD TYPE: L10V,K20M,L24I,S37D,M46I,I54V,L63P,A71V,V82T THERE IS ONE PROTEASE DIMER IN AN ASYMMETRICAL UNIT. THE TWO MOLECULES ARE LABELED AS CHAIN A AND CHAIN B. THERE IS ONE L-735,524 INHIBITOR MOLECULE LABELED AS MK1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: otherDetails: inhibitor-protein mixture and the reservoir solution were mixed in a 1:1(v/v) ratio | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | Num. all: 35099 / Num. obs: 7254 / % possible obs: 89 % / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 84 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. measured all: 35099 |
Reflection shell | *PLUS % possible obs: 84 % / Num. unique obs: 676 / Num. measured obs: 1775 / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 4.4 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→8 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.18 / Rfactor obs: 0.18 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|